Sunday, September 11, 2011

So I thought I'd just write down what I'm working on for the average person who's curious. I work on an instrument called a magnetic tweezer. We use magnetic tweezers to study biophysics. We can take a single strand of DNA and bond a magnetic bead to one end of the DNA and a glass slide to the other. Since the bead is paramagnetic, we can stretch a single strand of DNA when we bring a magnet close by. By changing the distance of the external magnet we can change the force on the DNA, and thus we can do force spectroscopy (a fancy word for measuring DNA length as a function of force). Within the Saleh Lab where I work, there are a few main topics of research using magnetic tweezers: ion-DNA interactions, DNA-DNA interactions, and protein-DNA interactions.

I work on protein-DNA interactions. Specifically, I am interested in a class of proteins called helicases. These proteins unzip genes and are therefore the subject of many biology-related pickup lines. Perhaps even more interesting is that they are involved in replication and all sorts of biological functions. You have trillions and trillions of helicase molecules in your body. Helicases are the bulldozer at the front of the replication machinery. We have classified a bunch of different types of helicases, but we don't yet understand how helicases move. We know that they burn ATP, but do they take single base-pair step for each ATP consumed? Or do they take steps of multiple base-pairs? Right now we don't know, and I hope to use magnetic tweezers to measure the step-size of helicase molecules.

There are numerous technical challenges standing in the way of answering fundamental questions about how helicases move along DNA. First of all, we can't actually see the DNA or the helicase. All we can see is the magnetic bead and use that bead as a probe to deduce the position of the protein. We typically use a hairpin of DNA, whereby each base-pair that is unzipped results in the magnetic bead moving towards the magnets by about 0.6 nanometers per base-pair unzipped. To put that in perspective: that's very small!

Measuring helicase steps are further complicated by the fact that the magnetic beads are undergoing Brownian motion from being bumped around by the surrounding water molecules. So when we see the bead move, we never really know for sure if it was because the helicase unzipped a single base-pair or if the water molecules bumped the bead and stretched the DNA a bit. The only way to get around the thermal noise is to take lots of measurements and average out the noise. So that's the reason I have been playing with a high-speed camera a lot lately. Oh, and everything is cooler in sloooowww moootttiiiooonnnn.

I'm trying to make the best of your tax-payer dollars, but if you have any questions or comments I'd be happy to hear them.